Have you read a cool paper recently that you want to discuss?

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Have you recently published something you want to brag on?

Share them here and get the discussion started!

This is an old homework question, so I've already gotten this wrong and just want to know why.

The question asked about the sigmoidal nature of the hemoglobin binding graph - and what exactly that shows about hemoglobin's binding.

The answer was cooperative binding, when I said allosteric binding (which was incorrect). Does "allosteric" only refer to the fact that there is a conformational change when one subunit binds oxygen, and doesn't actually describe the cooperative nature of the protein?

Lomeguatrib is a potent inhibitor of O6-alkylguanine-DNA-alkyltransferase which itself is the basis of snap-tags (with modifications to improved stability etc). I'd prefer to buy lomeguatrib over New England Biolab's snap-cell block because its way cheaper and structurally almost identical aside from the 5 member ring versus 6 member ring difference. Furthermore, most of their products are 5 member fused with 6 member ring structures (O6-Benzylguanine) as opposed to 2 fused 6 member ring structures (only their snap-cell block).

My suspicion is that they only invented snap-cell block to have something that is patented by them and thus is restricted to only them for sale (for a lot higher price and for very limited reagent) and that I can just as easily just use the chemotherapy lomeguatrib instead.

I'm just wondering if anyone has any experience in this.

Hi I am planning to generate a blood cell line with 3 genes (those 3 genes are like protein isoforms) stably knocked-down. As I am new to RNAi, I have generated 3 shRNAs for each gene and cloned to a shRNA vector. After screening for the best shRNA, I plan to nucleofect all 3 at once, but problem is all of them have puromycin resistance gene, so there maybe only 1-2 shRNAs entered the majority of the cells.

Another idea is cloning all 3 shRNAs into a multi-shRNA vector, which seems to be a better option. However, I don't have a clear picture on how to do this, or at least finding a vector for this. Any ideas on this? Thanks!

I am looking to produce a protein complex with 14 subunits that will need to be co-expressed. The company I typically use says that production of a single plasmid with more than 4 genes is outside of their capabilities. Does anyone on here have experience with a company that might be able to handle such a request? Any help would be greatly appreciated.

So I've been learning about Blood Coagulation, and I've finally understood this cascaded pathway except for one small clarification. Are the proteins that have question mark on the upper left side present by default in the blood plasma? The proteins I've marked with a correct sign are those that the textbook confirmed to be present already in the blood plasma.

Any insights will be greatly appreciated, thanks!

Hey everyone! I’m a biochemistry graduate currently applying for PhD programs. I have a couple of questions: What fields do you think would be best for my qualifications, and which ones might offer an easier transition to industry from academia? I’d appreciate any insights, but please avoid the typical advice to just follow my interests—I’ve seen many scholars end up disliking subjects they once loved. Thanks!

I recently learned that Baker lab is using using diffusion models to generate novel protein 3d structures then using alphafold to predict possible sequences. But I don't see how that's possible when it was trained only on sequences of known proteins and, as far as I am aware, can only predict the structures of related proteins.

I'm interested in the plant thelesperma megapotamicum. I've read that it has caffeine, but that doesn't align with my experience of drinking it as tea. I'd like to know:

• What is the caffeine concentration in the dried plant matter?
• What other alkaloids are present?
• What is the concentration of the other alkaloids? (less important until I know what's present)

I found some commercial services, but you need to talk to a salesperson to get the full info. I thought I'd ask some impartial people before I do that.

I've only found two papers with analysis of the plant, Occurrence and Risk of Metal(loid)s in Thelesperma megapotamicum Tea Plant and Polyphenols from Thelesperma megapotamicum and Their Antioxidant and Neuroprotective Activities.

Thanks in advance for any help.

Hey all, I hope I’m in the right sub-Reddit, but here goes.

So I’m a respiratory therapist, and I was approached by dietary about how much carbohydrates within a patients feeding can we give before we raise the CO2 and we have to start making vent adjustments? Well….. I have no clue!! So I guess my question is is there a calculation to figure this out, or at least can someone point me in the right direction?

This is honestly a sanity check. Someone I know recombinantly expressed a protein with a randomized sequence. They took a natural protein, randomized the sequence and expressed it. And for some reason everyone is surprised it's entirely insoluble. My thinking, no folding equals = aggregation. Is this an unreasonable assertion, or is there something I'm missing?

I’m trying to put together a safe lipid TLC lab for undergrads. I would like to use ethanol as the solvent on a silica gel solid phase and maybe just have them run some standards (for example: cholesterol, palmitic acid). Does anyone know of a protocol like this? Or another very safe lipid analysis lab appropriate to undergraduate students?

Edit: Alternatively, any labs where you just use standards (as those mentioned above) on a TLC plate??

I am graduating with a Biochemistry ACS degree in May. I’ve done 9 credit hours worth of undergraduate research, and am a student worker in a lab. My GPA is not the greatest, though, it’s sitting right at 2.96, although after this semester it will likely be a 3.1-3.15. How screwed am I, if at all? And do any of you have any advice or insight to share about searching for jobs following graduation. I’ve only applied to 50 so far.

So, I am trying to express a protein in BL21(DE3). Last year, I was able to express it with no issues. This year, things had gone very bad with my lab’s glycerol stock of the cells, so we got a new one; however under the same growth conditions, I am now getting no protein. I have troubleshooted many things, but there is prob one thing I haven’t tested yet. SDS-PAGE is what I use to confirm for protein. Protein is soluble in water. I listed below how I grow them before and what I tested. Any help would be appreciated!

Before problem: 37C growth until OD600 0.4-0.6, followed by 20C growth with 16-18 hour induction, 1 mM IPTG, and 160 rpm

What I’ve tested:

• different temperature 20C vs 37C (3hr growth)

-different media reagents from different company -different IPTG stocks -different ITPG concentrations (1 mM vs 0.5 mM) -swapped from ampicillin to carbenicillin (which helped give a little more expression, but not much as before) -competent cells shelf life (one day vs one week vs 1 month) -different cell stocks of BL21(DE3) from different labs

Hi everyone,

 I'm considering applying to the Biochemistry PhD program at Duke University and would love to hear from current or former students about their experiences. What are the pros and cons of the program? Any insights on the faculty, research opportunities, lab culture, and overall experience would be greatly appreciated!

Thanks in advance!

Which of the 2 structures is true? Let me explain further. In the notes I have that in the beta structure, each edge is represented by an alpha carboin, as confirmed in the first picture. However, in the second picture each edge is represented by an atom

https://preview.redd.it/y65zrf8qtiwd1.png?width=549&format=png&auto=webp&s=58aff8de6b4b742a96f6b84211d7c3f62dfedbcc

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

As someone graduating soon, what are my odds of getting a decent job out of undergrad or should I immediately go into higher education?

Hi, I'm a junior biochem major and need to take physics 1 and 2. But I have the option to take algebra based physics or calculus based physics. I know the calculus one is harder but do grad schools care about which one I should take? And would they require a physics lab?

https://preview.redd.it/950bt5c5kcwd1.png?width=1375&format=png&auto=webp&s=022fb8fec71732660721db9d5e5086555fc07441

Talking to my mentor in my research lab, she told me that Id be better off pursuing math since biological sciences are pretty bad. Ive lived close to Boston for most of my life and I have really enjoyed researching Metabolomics this past semester but should I consider doing math instead? I also have a good intuition for math (better than biochem) but I don’t like it quite as much as Biochemistry. Im not afraid of having to go to some kind of graduate school as that has kinda been the plan so far after I graduate, however I dont want to waste my time if finding jobs in industry is difficult despite living near Boston already.

I should note that I am a Sophomore at an R1 institute however far from any urban centers so I have the opportunity to get good research experience but no good internships during the year. Ive been focusing heavily on math anyways since Im already planning a minor and I need to finish orgo 2 this semester to start any formal Biochem coursework. Ive only started my research lab this year which is most just analytics then any real bench work, also pursuing a 1 semester class on phage gene annotations for my name to be on some kind of formal research paper, and Ive tried my best at maintaining a good gpa ~3.8, however I dont know what else I should be doing in order to find success

After doing a bit of research, the companies that come to mind in Europe are.

Ella Biotech GmbH (Germany)

Microsynth (Switzerland)

Biomers (Germany)

Eurogentec (Belgium)

Does anyone here have any experience ordering oligos from these companies? Especially modified RNAs for siRNA or ASO applications?

Thanks guys

Hi friends, accounting major here. Throughout my life, I have always been interested in chemistry and I excelled in organic chemistry, high level calculus and physics. However, due to financial reasons I chose to pivot to accounting. I already have a job lined up in tax consulting and I expect to make 85k upon graduation; but I don’t know, I don’t feel passionate about accounting. Maybe I’m just feeling the “what if” syndrome now that I’m almost done with college, but I feel as if I made a mistake in not pursuing biochemistry. I know biochem is hard, and I know you will typically need to go to graduate school to get into higher pay grades. I don’t plan on changing my major now, let’s say I decide to go back to school in the future, Is it too late?

Now onto the mecs for the gluconeogenesis bypasses, TCA, & ETC.